PRS Knowledge Base

PRS Knowledge Base integrates NHGRI-EBI GWAS Catalog associations and computes sample-specific polygenic risk scores to contextualize genetic risk across reference cohorts.


Key Features:

  • GWAS integration: Integrates over 250,000 genetic variant associations from the NHGRI-EBI GWAS Catalog.
  • Centralized repository: Aggregates variant-level association data into a centralized repository for PRS computation.
  • Data harmonization: Identifies appropriate genome-wide association (GWA) studies and formats and harmonizes variant data for PRS computation.
  • PRS calculation: Calculates sample-specific polygenic risk scores using GWAS-derived effect sizes.
  • Contextualization and comparability: Contextualizes computed PRS within reference cohorts and compares results to those from other PRS tools to support reproducibility.

Scientific Applications:

  • Quantification of genetic risk: Computes PRS across studies to quantify genetic predisposition to disease.
  • Cohort contextualization: Places individual or sample PRS in the context of reference datasets such as UK Biobank, 1000 Genomes Project, and the Alzheimer's Disease Neuroimaging Initiative (ADNI).
  • Complex disease research and confounder identification: Supports investigation of potentially confounding genetic risk factors in complex diseases, including Alzheimer's disease.

Methodology:

Integrates >250,000 NHGRI-EBI GWAS Catalog associations, identifies appropriate GWA studies, formats and harmonizes variant data for PRS computation, computes sample-specific polygenic risk scores using GWAS effect sizes, and performs contextual comparisons to reference cohorts and other PRS tools.

Topics

Details

Cost:
Free of charge
Tool Type:
web application
Operating Systems:
Mac, Linux, Windows
Added:
11/5/2022
Last Updated:
11/24/2024

Operations

Publications

Page ML, Vance EL, Cloward ME, Ringger E, Dayton L, Ebbert MTW, Weiner MW, Aisen P, Petersen R, Jack CR, Jagust W, Trojanowki JQ, Toga AW, Beckett L, Green RC, Saykin AJ, Morris JC, Perrin RJ, Shaw LM, Khachaturian Z, Carrillo M, Potter W, Barnes L, Bernard M, González H, Ho C, Hsiao JK, Jackson J, Masliah E, Masterman D, Okonkwo O, Perrin R, Ryan L, Silverberg N, Fleisher A, Sacrey DT, Fockler J, Conti C, Veitch D, Neuhaus J, Jin C, Nosheny R, Ashford M, Flenniken D, Kormos A, Monine T, Rafii M, Raman R, Jimenez G, Donohue M, Gessert D, Salazar J, Zimmerman C, Cabrera Y, Walter S, Miller G, Coker G, Clanton T, Hergesheimer L, Smith S, Adegoke O, Mahboubi P, Moore S, Pizzola J, Shaffer E, Sloan B, Harvey D, Forghanian-Arani A, Borowski B, Ward C, Schwarz C, Jones D, Gunter J, Kantarci K, Senjem M, Vemuri P, Reid R, Fox NC, Malone I, Thompson P, Thomopoulos SI, Nir TM, Jahanshad N, DeCarli C, Knaack A, Fletcher E, Tosun-Turgut D, Chen SR, Choe M, Crawford K, Yushkevich PA, Das S, Koeppe RA, Reiman EM, Chen K, Mathis C, Landau S, Cairns NJ, Householder E, Franklin E, Bernhardt H, Taylor-Reinwald L, Shaw LM, Tojanowki JQ, Korecka M, Figurski M, Crawford K, Neu S, Nho K, Risacher SL, Apostolova LG, Shen L, Foroud TM, Nudelman K, Faber K, Wilmes K, Winer MW, Thal L, Hsiao JK, Silbert LC, Lind B, Crissey R, Kaye JA, Carter R, Dolen S, Quinn J, Schneider LS, Pawluczyk S, Becerra M, Teodoro L, Dagerman K, Spann BM, Brewer J, Vanderswag H, Fleisher A, Ziolkowski J, Heidebrink JL, Zbizek-Nulph L, Lord JL, Mason SS, Albers CS, Knopman D, Johnson K, Villanueva-Meyer J, Pavlik V, Pacini N, Lamb A, Kass JS, Doody RS, Shibley V, Chowdhury M, Rountree S, Dang M, Stern Y, Honig LS, Mintz A, Ances B, Winkfield D, Carroll M, Stobbs-Cucchi G, Oliver A, Creech ML, Mintun MA, Schneider S, Geldmacher D, Love MN, Griffith R, Clark D, Brockington J, Marson D, Grossman H, Goldstein MA, Greenberg J, Mitsis E, Shah RC, Lamar M, Samuels P, Duara R, Greig-Custo MT, Rodriguez R, Albert M, Onyike C, Farrington L, Rudow S, Brichko R, Kielb S, Smith A, Raj BA, Fargher K, Sadowski M, Wisniewski T, Shulman M, Faustin A, Rao J, Castro KM, Ulysse A, Chen S, Sheikh MO, Singleton-Garvin J, Doraiswamy PM, Petrella JR, James O, Wong TZ, Borges-Neto S, Karlawish JH, Wolk DA, Vaishnavi S, Clark CM, Arnold SE, Smith CD, Jicha GA, Khouli RE, Raslau FD, Lopez OL, Oakley M, Simpson DM, Porsteinsson AP, Martin K, Kowalski N, Keltz M, Goldstein BS, Makino KM, Ismail MS, Brand C, Thai G, Pierce A, Yanez B, Sosa E, Witbracht M, Kelley B, Nguyen T, Womack K, Mathews D, Quiceno M, Levey AI, Lah JJ, Hajjar I, Cellar JS, Burns JM, Swerdlow RH, Brooks WM, Silverman DHS, Kremen S, Apostolova L, Tingus K, Lu PH, Bartzokis G, Woo E, Teng E, Graff-Radford NR, Parfitt F, Poki-Walker K, Farlow MR, Hake AM, Matthews BR, Brosch JR, Herring S, van Dyck CH, Mecca AP, Good SP, MacAvoy MG, Carson RE, Varma P, Chertkow H, Vaitekunis S, Hosein C, Black S, Stefanovic B, Heyn C, Hsiung GR, Kim E, Mudge B, Sossi V, Feldman H, Assaly M, Finger E, Pasternak S, Rachinsky I, Kertesz A, Drost D, Rogers J, Grant I, Muse B, Rogalski E, Robson J, Mesulam M, Kerwin D, Wu C, Johnson N, Lipowski K, Weintraub S, Bonakdarpour B, Pomara N, Hernando R, Sarrael A, Rosen HJ, Miller BL, Perry D, Turner RS, Johnson K, Reynolds B, McCann K, Poe J, Sperling RA, Johnson KA, Marshall GA, Yesavage J, Taylor JL, Chao S, Coleman J, White JD, Lane B, Rosen A, Tinklenberg J, Belden CM, Atri A, Spann BM, Clark KA, Zamrini E, Sabbagh M, Killiany R, Stern R, Mez J, Kowall N, Budson AE, Obisesan TO, Ntekim OE, Wolday S, Khan JI, Nwulia E, Nadarajah S, Lerner A, Ogrocki P, Tatsuoka C, Fatica P, Fletcher E, Maillard P, Olichney J, DeCarli C, Carmichael O, Bates V, Capote H, Rainka M, Borrie M, Lee T, Bartha R, Johnson S, Asthana S, Carlson CM, Perrin A, Burke A, Scharre DW, Kataki M, Tarawneh R, Kelley B, Hart D, Zimmerman EA, Celmins D, Miller DD, Ponto LLB, Smith KE, Koleva H, Shim H, Nam KW, Schultz SK, Williamson JD, Craft S, Cleveland J, Yang M, Sink KM, Ott BR, Drake JD, Tremont G, Daiello LA, Sabbagh M, Ritter A, Bernick C, Munic D, Mintz A, O’Connell A, Mintzer J, Williams A, Masdeu J, Shi J, Garcia A, Sabbagh M, Newhouse P, Potkin S, Salloway S, Malloy P, Correia S, Kittur S, Perlson GD, Blank K, Anderson K, Flashman LA, Seltzer M, Hynes ML, Santulli RB, Relkin N, Chiang G, Lee A, Lin M, Ravdin L, Miller JB, Kauwe JSK. The Polygenic Risk Score Knowledge Base offers a centralized online repository for calculating and contextualizing polygenic risk scores. Communications Biology. 2022;5(1). doi:10.1038/s42003-022-03795-x. PMID:36056235. PMCID:PMC9438378.

PMID: 36056235
PMCID: PMC9438378
Funding: - BrightFocus Foundation: A2020118F, A2020161S - U.S. Department of Health & Human Services | NIH | National Institute on Aging: 1P30AG072946-01, AG068331, RF1AG054052 - U.S. Department of Health & Human Services | NIH | National Institute of General Medical Sciences: GM138636 - Alzheimer's Association: 2019-AARG-644082